Datasets:

junidude14
/

PBISC-data

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_extra_slide_text.json ADDED Viewed

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+{
+ "section": "09-extra",
+ "slides": [
+  {
+   "title": "5 donors: realism beyond precision/coverage",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_extra_fewpair.png"
+   ],
+   "keywords": [
+    "Classifier AUC: LoRA-5 best in 25/25 draws",
+    "E_N: LoRA-5 below scSemi-5 in 25/25 draws",
+    "Still separable: LoRA-5 AUC 0.89–0.95"
+   ],
+   "footnote": "Same 5-donor draws as the previous slides; every metric on exactly the scored cells (scores_extra/, tools/extra_metrics.py). Real side for AUC and MMD² = held-out real cells of the same samples (R2), projected like the generated cells; real vs real = R2 vs R3 (AUC 0.49–0.50). Classifier AUC: 5-fold CV ROC AUC of a kNN classifier (k = 5) separating real from generated cells, 0.5 = indistinguishable; bars start at 0.5. MMD²: unbiased, Gaussian kernel, bandwidth = median distance among real cells. E_N: scSemiProfiler's normalized error (Wang et al. 2024, eq. 17–18), their code's squared L2 on all cells, per-arm PCA-100; real vs real = within-sample half split (0.07–0.38); every generated arm is above 1. LoRA-5 best of the 4 arms in 25/25 draws on kNN AUC, 25/25 on RF AUC, 25/25 on 1-NN accuracy, 23/25 on MMD², 22/25 on E_N. LoRA-5 better than scSemi-5, zero-shot and zero-shot + calibration on both AUCs, 1-NN accuracy and coverage at k = 3, 5, 10 in every draw. E_N scSemi-5 vs LoRA-5 (cohort means): ImMicro 3.65 vs 1.55; Sepsis 3.83 vs 1.46; Imperial 2.04 vs 1.28; Giroux 3.79 vs 1.99; Ji 4.27 vs 2.60; LoRA-5 lower in 25/25 draws. Draws where LoRA-5 is worse (cohort means in brackets): vs zero-shot + calibration: Sepsis precision k5 1/5 (0.778 vs 0.752), precision k10 2/5 (0.906 vs 0.899); Imperial MMD² (σ = m) 1/5 (0.0156 vs 0.0218), MMD² (σ sum) 1/5 (0.0443 vs 0.0673), E_N (all cells) 3/5 (1.28 vs 1.22), precision k3 2/5 (0.610 vs 0.598), precision k5 2/5 (0.726 vs 0.719), precision k10 2/5 (0.853 vs 0.845); Giroux MMD² (σ = m) 1/5 (0.0178 vs 0.0257), MMD² (σ sum) 1/5 (0.0584 vs 0.0838), precision k5 1/5 (0.995 vs 0.981), precision k10 1/5 (1.000 vs 0.996). LoRA-5 AUC per draw 0.88–0.97 (kNN), RF cohort means 0.90–0.96: a classifier still tells generated from real cells. Scores: scores_extra/<cohort>/fewshot_n5/draw<j>/.",
+   "footnote_short": "E_N: scSemiProfiler's own error metric. Misses only vs calibration, e.g. Imperial E_N 1.28 vs 1.22.",
+   "numbers": [
+    {
+     "value": "LoRA-5 best of 4 arms (draws): kNN AUC 25/25, RF AUC 25/25, 1-NN 25/25, MMD² 23/25, E_N 22/25",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/<cohort>/fewshot_n5/draw<j>/{metrics,en}.csv"
+    },
+    {
+     "value": "E_N LoRA-5 < scSemi-5 in 25/25 draws; cohort means scSemi-5 vs LoRA-5: ImMicro 3.65 vs 1.55; Sepsis 3.83 vs 1.46; Imperial 2.04 vs 1.28; Giroux 3.79 vs 1.99; Ji 4.27 vs 2.60",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/<cohort>/fewshot_n5/draw<j>/en.csv (cellset all, distance sq)"
+    },
+    {
+     "value": "LoRA-5 kNN AUC cohort means: ImMicro 0.943, Sepsis 0.936, Imperial 0.918, Giroux 0.893, Ji 0.955; per draw 0.878–0.975",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/<cohort>/fewshot_n5/draw<j>/{metrics,en}.csv"
+    },
+    {
+     "value": "real vs real: kNN AUC ImMicro 0.502, Sepsis 0.501, Imperial 0.498, Giroux 0.495, Ji 0.491; E_N ImMicro 0.382, Sepsis 0.100, Imperial 0.260, Giroux 0.145, Ji 0.073",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/<cohort>/fewshot_n5/draw<j>/{metrics,en}.csv"
+    },
+    {
+     "value": "LoRA-5 worse than a comparator (draws): vs zero-shot + calibration: Sepsis precision k5 1/5 (0.778 vs 0.752), precision k10 2/5 (0.906 vs 0.899); Imperial MMD² (σ = m) 1/5 (0.0156 vs 0.0218), MMD² (σ sum) 1/5 (0.0443 vs 0.0673), E_N (all cells) 3/5 (1.28 vs 1.22), precision k3 2/5 (0.610 vs 0.598), precision k5 2/5 (0.726 vs 0.719), precision k10 2/5 (0.853 vs 0.845); Giroux MMD² (σ = m) 1/5 (0.0178 vs 0.0257), MMD² (σ sum) 1/5 (0.0584 vs 0.0838), precision k5 1/5 (0.995 vs 0.981), precision k10 1/5 (1.000 vs 0.996)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/<cohort>/fewshot_n5/draw<j>/{metrics,en}.csv"
+    },
+    {
+     "value": "cross-check: 720 cohort × arm × metric values equal scores_extra/{fewshot,pooled}_headline.csv",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/fewshot_headline.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/pooled_headline.csv"
+    }
+   ]
+  },
+  {
+   "title": "5-fold: realism beyond precision/coverage",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_extra_fivefold.png"
+   ],
+   "keywords": [
+    "Every metric: LoRA first in 5/5 cohorts",
+    "Ji whole blood: E_N 1.9 vs 4.1–10.1",
+    "Still separable: LoRA AUC 0.87–0.94"
+   ],
+   "footnote": "Donor-level 5-fold CV; each pair scored once by the fold model that never trained on its donor (one pooled call per cohort, all cross-fitted pairs). Arms as on the 5-fold slide. Metric definitions as on the 5-donor realism slide. LoRA first among the 5 arms in all 5 cohorts on 12/12 headline metrics (kNN and RF AUC, 1-NN accuracy, MMD² at σ = m and summed, E_N all cells, precision and coverage at k = 3, 5, 10). LoRA kNN AUC ImMicro 0.941, Sepsis 0.886, Imperial 0.866, Giroux 0.881, Ji 0.908; real vs real ImMicro 0.505, Sepsis 0.506, Imperial 0.496, Giroux 0.501, Ji 0.494. E_N LoRA vs other arms: ImMicro 1.56 vs 1.77–4.83; Sepsis 1.20 vs 1.40–5.29; Imperial 1.13 vs 1.19–4.05; Giroux 1.70 vs 2.24–4.48; Ji 1.95 vs 4.13–10.13. scSemiProfiler, 5-fold CV (every training donor of the fold, inner-val included, as representatives; arm scsemi__raw) drawn for ImMicro, Sepsis, Giroux, Ji; sources: ImMicro /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/immicro/scsemi_cv_20261002/pooled; Sepsis /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/ye2026_sepsis/scsemi_cv_20261002/pooled; Giroux /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/giroux2022/scsemi_cv_20261002/pooled; Ji /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/ji2025_chili/scsemi_cv_20261002/pooled. Scores: scores_extra/<cohort>/pooled/.",
+   "footnote_short": "Donor-level 5-fold CV, one pooled call per cohort. E_N: scSemiProfiler's own error metric.",
+   "numbers": [
+    {
+     "value": "LoRA first among 5 arms in all 5 cohorts on 12/12 metrics",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/<cohort>/pooled/{metrics,en}.csv"
+    },
+    {
+     "value": "Ji E_N: LoRA 1.948; Zero-shot, real bulk 10.125, Zero-shot + calibration 7.076, sc-only fine-tune (+ calibration) 7.215, scSemiProfiler, 5-fold CV (other 4 folds) 4.132",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/<cohort>/pooled/{metrics,en}.csv"
+    },
+    {
+     "value": "LoRA kNN AUC (pooled): ImMicro 0.941, Sepsis 0.886, Imperial 0.866, Giroux 0.881, Ji 0.908",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/<cohort>/pooled/{metrics,en}.csv"
+    },
+    {
+     "value": "scSemiProfiler, 5-fold CV: ImMicro, Sepsis, Giroux, Ji",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec09_extra_scsemi_status.csv"
+    }
+   ]
+  },
+  {
+   "title": "5 donors: precision/coverage at k = 3, 5, 10",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_extra_ksens.png"
+   ],
+   "keywords": [
+    "Smaller k lowers every set, real included",
+    "Coverage: LoRA-5 first at all k, 25/25",
+    "Precision: LoRA-5 first in 20–23/25 draws"
+   ],
+   "footnote": "Precision and coverage recomputed with k = 3, 5, 10 nearest-neighbour balls in the scorer's PCA-50 (k = 10 reproduces the main-slide values exactly). Means over the 5 draws per cohort; error bars = SD; grey = real vs real (R1 vs R2, same samples). Both metrics fall with smaller k for every set including the real control (real coverage at k = 3: 0.92–0.99), so compare arms with the real row, not with 1. Expected coverage of a perfect generator (Naeem et al. 2020, eq. 9) at k = 3/5/10: 0.88/0.97/1.00 in every cohort. LoRA-5 first on coverage at every k in 25/25 draws; on precision in 23/21/20 of 25 draws (k = 3/5/10); not first: Sepsis 0/1/2, Imperial 2/2/2, Giroux 0/1/1 draws at k = 3/5/10, beaten by zero-shot + calibration. 5-fold pooled design (not drawn): coverage ranking of the 5 arms across k unchanged; LoRA first at every k in 5/5 cohorts. Scores: scores_extra/<cohort>/fewshot_n5/draw<j>/metrics.csv.",
+   "footnote_short": "5 donors, 5 draws per cohort; error bars = SD over draws. k = 10 is the value on the main slides.",
+   "numbers": [
+    {
+     "value": "LoRA-5 first on coverage at k = 3, 5 and 10: 25/25 draws",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/<cohort>/fewshot_n5/draw<j>/{metrics,en}.csv"
+    },
+    {
+     "value": "LoRA-5 first on precision (draws) at k = 3/5/10: 23/21/20 of 25",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/<cohort>/fewshot_n5/draw<j>/{metrics,en}.csv"
+    },
+    {
+     "value": "real vs real coverage at k = 3: ImMicro 0.932, Sepsis 0.925, Imperial 0.919, Giroux 0.993, Ji 0.980",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/<cohort>/fewshot_n5/draw<j>/{metrics,en}.csv"
+    },
+    {
+     "value": "every set falls with smaller k (cohort means): True",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_extra/<cohort>/fewshot_n5/draw<j>/{metrics,en}.csv"
+    }
+   ]
+  }
+ ],
+ "scripts": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/sec09_extra_metrics.py"
+ ],
+ "generated_from": "tools/sec09_extra_metrics.py (rerun to refresh; do not edit by hand)",
+ "scsemi_cv_cohorts": [
+  "ImMicro",
+  "Sepsis",
+  "Giroux",
+  "Ji"
+ ]
+}

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_same_pairs_slide_text.json ADDED Viewed

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+{
+ "section": "09-same-pairs",
+ "scripts": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/sec09_same_pairs.py"
+ ],
+ "generated_from": "tools/sec09_same_pairs.py (rerun to refresh; do not edit by hand)",
+ "slides": [
+  {
+   "title": "Same training pairs: LoRA vs scSemiProfiler",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_same_pairs.png"
+   ],
+   "keywords": [
+    "Coverage, precision: LoRA ahead in 4/4",
+    "LoRA ahead in composition 3/4, logFC r 2/3",
+    "19–62× less GPU time per fold"
+   ],
+   "footnote_short": "5-fold CV; scSemiProfiler representatives = LoRA's training pairs. Imperial: running.",
+   "footnote": "5-fold CV: for every fold, scSemiProfiler's representatives are exactly LoRA's training + inner-val pairs (the other four folds; checked per fold), test = the fold's samples from their real bulk only. Pooled = one scoring call per method over every usable sample, same donors and reference (sha-checked). scSemiProfiler = upstream c2aea02, default settings, official output. GPU time per fold on one GB10: LoRA = fine-tune + sampling 1,500 cells per test sample; scSemiProfiler = pretraining of every representative + one model per test sample (receipts); data preparation and scoring not counted on either side. scSemiProfiler ahead on composition: Giroux. scSemiProfiler ahead on logFC r: Giroux. Still running (server_1 / server_2): Imperial. Equal pair budget, ImMicro (n = 5, 10, 20, 40 pairs): scSemiProfiler L1 0.218–0.227 and coverage 0.04–0.04 at every n; LoRA L1 0.171–0.188, coverage 0.76–0.84 (drawn on the 'Pairs needed: composition, coverage, training steps' slide). Equal pair budget, Sepsis (n = 5, 10, 20, 40 pairs): scSemiProfiler L1 0.516–0.536 and coverage 0.10–0.10 at every n; LoRA L1 0.365–0.428, coverage 0.77–0.82 (drawn on the 'Pairs needed: composition, coverage, training steps' slide). Source: plans/paired_finetune_intradataset_20260927/scores/<cohort>/{pooled,scsemi_cv_20261002/pooled}/ and scsemi/analysis/cv_budget_20261005/.",
+   "numbers": [
+    {
+     "value": "ImMicro: L1 LoRA 0.162 / scSemi 0.217; coverage 0.784 / 0.038; precision 0.924 / 0.505; logFC r nan / nan; top-50 DEG None / None; GPU per fold LoRA 14.7 min / scSemi 4.75 h",
+     "source": "data/sec09_same_pairs.csv"
+    },
+    {
+     "value": "Sepsis: L1 LoRA 0.362 / scSemi 0.502; coverage 0.829 / 0.096; precision 0.926 / 0.760; logFC r 0.527 / 0.435; top-50 DEG 23 / 6; GPU per fold LoRA 7.4 min / scSemi 7.69 h",
+     "source": "data/sec09_same_pairs.csv"
+    },
+    {
+     "value": "Giroux: L1 LoRA 0.258 / scSemi 0.243; coverage 0.928 / 0.354; precision 0.998 / 0.872; logFC r 0.461 / 0.537; top-50 DEG 5 / 0; GPU per fold LoRA 3.6 min / scSemi 2.89 h",
+     "source": "data/sec09_same_pairs.csv"
+    },
+    {
+     "value": "Ji: L1 LoRA 0.504 / scSemi 0.575; coverage 0.857 / 0.167; precision 0.971 / 0.858; logFC r 0.479 / 0.273; top-50 DEG 15 / 0; GPU per fold LoRA 4.4 min / scSemi 1.48 h",
+     "source": "data/sec09_same_pairs.csv"
+    },
+    {
+     "value": "Equal pair budget, ImMicro (n = 5, 10, 20, 40 pairs): scSemiProfiler L1 0.218–0.227 and coverage 0.04–0.04 at every n; LoRA L1 0.171–0.188, coverage 0.76–0.84 (drawn on the 'Pairs needed: composition, coverage, training steps' slide). Equal pair budget, Sepsis (n = 5, 10, 20, 40 pairs): scSemiProfiler L1 0.516–0.536 and coverage 0.10–0.10 at every n; LoRA L1 0.365–0.428, coverage 0.77–0.82 (drawn on the 'Pairs needed: composition, coverage, training steps' slide).",
+     "source": "data/sec09_same_pairs_budget.csv"
+    }
+   ]
+  }
+ ]
+}

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_slide_text.json ADDED Viewed

	@@ -0,0 +1,290 @@

+{
+ "section": "09",
+ "slides": [
+  {
+   "title": "Five paired cohorts",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_cohorts.png"
+   ],
+   "keywords": [
+    "403 paired samples, 275 donors",
+    "Only identity-pass pairs; donor-level splits",
+    "Ji bulk: whole blood, not PBMC"
+   ],
+   "footnote": "Usable pair = passed the pairing identity check and >= 200 cells (fold >= 0 in data/<cohort>/folds.csv); dropped 15 identity-fail, 11 borderline and 1 low-cell pairs of 430. ImMicro: no identity flag, all used. Imperial, Giroux, Ji: several pairs per donor. Case vs control = samples in scores/<cohort>/pooled/summary.json. Giroux 'moderate' = GEO 'severe' (paper term); its moderate vs mild subjects are 4F/0M vs 0F/5M (scored), so its disease metrics exclude sex-linked genes. Labels: data/<cohort>/QC_REPORT.md; ImMicro: GEO GSE314922/GSE314416.",
+   "footnote_short": "Usable pair = passed identity check and ≥ 200 cells: 403 of 430 pairs; donor-level splits.",
+   "numbers": [
+    {
+     "value": "403 paired samples (sum of usable rows)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/fewshot_n5/DRAWS.json (n_usable_rows)"
+    },
+    {
+     "value": "275 donors (sum of usable donors)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/fewshot_n5/DRAWS.json (n_usable_donors)"
+    },
+    {
+     "value": "dropped 15 identity-fail, 11 borderline, 1 < 200 cells, of 430",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/features.npz (identity_pass, identity_check); samples.csv (n_cells); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/prepare_dataset.py (MIN_CELLS)"
+    },
+    {
+     "value": "ImMicro 107 pairs / 107 donors",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/fewshot_n5/DRAWS.json"
+    },
+    {
+     "value": "Sepsis 82 pairs / 82 donors; sepsis 61 vs control 21",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fewshot_n5/DRAWS.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json"
+    },
+    {
+     "value": "Imperial 157 pairs / 57 donors; COVID+ 113 vs COVID− 34 (+10 recovery, neither)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/fewshot_n5/DRAWS.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/pooled/summary.json"
+    },
+    {
+     "value": "Giroux 24 pairs / 9 donors; moderate 11 vs mild 13",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fewshot_n5/DRAWS.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/pooled/summary.json"
+    },
+    {
+     "value": "Ji 33 pairs / 20 donors; ChILI 18 vs ICI control 15",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/fewshot_n5/DRAWS.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled/summary.json"
+    }
+   ]
+  },
+  {
+   "title": "5 donors: LoRA vs scSemiProfiler — cells",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_fewpair_cells.png"
+   ],
+   "keywords": [
+    "LoRA-5 > scSemi-5: coverage, precision 5/5",
+    "Beats zero-shot + calibration: coverage 5/5",
+    "Lower L1 than calibration: ImMicro only"
+   ],
+   "footnote": "Base f01 6k·1x·E16 (EMA, DDIM 50) + LoRA r=16, 3,000 steps. LoRA-5 / scSemi-5 = LoRA / scSemiProfiler trained on the same 5 donors (5–15 pairs); test = all other usable pairs. Zero-shot = base model without fine-tuning, fed each test pair's real bulk as measured; zero-shot + calibration = the same model fed that bulk after gene-wise calibration, alpha fitted on the same 5 training donors' pairs (both in the same call as LoRA-5). scSemi-5 scored in a separate call, same test set and reference (sha-checked); 25/25 draws. Verdict = better in >= 80% of shared draws. LoRA-5 lower L1 than scSemi-5 in 4/5 (Giroux split 3/5). LoRA-5 > zero-shot + calibration: coverage 5/5, precision 3/5, depth-matched 5/5 and 3/5 cohorts; > zero-shot (real bulk): coverage 5/5, precision 5/5, depth-matched 5/5 and 4/5. Depth-matched P/C vs scSemi-5: same ranking, coverage LoRA-5 0.83–0.97 vs scSemi-5 0.15–0.28. Composition L1, LoRA-5 minus zero-shot + calibration, per-donor Wilcoxon (gain = p < 0.05): ImMicro -0.03 (p 2e-10), Sepsis +0.02 (p 0.79), Imperial +0.02 (p 0.38), Giroux -0.06 (p 0.38), Ji -0.01 (p 0.70); minus zero-shot (real bulk): ImMicro -0.27 (p 2e-18), Sepsis -0.04 (p 0.15), Imperial -0.35 (p 2e-08), Giroux -0.11 (p 0.04), Ji -0.23 (p 0.02). scANVI labels; P/C = PCA-50, k=10 balls. Scores: scores/<cohort>/fewshot_n5/.",
+   "footnote_short": "5 draws per cohort; test = all other usable pairs. Calibration α from the same 5 donors. scANVI labels.",
+   "numbers": [
+    {
+     "value": "LoRA-5 vs scSemi-5 coverage (shared-draw means; LoRA-better draws/n; verdict): ImMicro 0.792 vs 0.036 (5/5, lora); Sepsis 0.694 vs 0.080 (5/5, lora); Imperial 0.737 vs 0.059 (5/5, lora); Giroux 0.961 vs 0.607 (5/5, lora); Ji 0.707 vs 0.145 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 vs scSemi-5 precision (shared-draw means; LoRA-better draws/n; verdict): ImMicro 0.952 vs 0.518 (5/5, lora); Sepsis 0.906 vs 0.728 (5/5, lora); Imperial 0.853 vs 0.330 (5/5, lora); Giroux 1.000 vs 0.992 (5/5, lora); Ji 0.978 vs 0.840 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 vs scSemi-5 comp_l1 (shared-draw means; LoRA-better draws/n; verdict): ImMicro 0.176 vs 0.233 (5/5, lora); Sepsis 0.466 vs 0.612 (5/5, lora); Imperial 0.503 vs 0.602 (5/5, lora); Giroux 0.256 vs 0.270 (3/5, split); Ji 0.513 vs 0.592 (4/5, lora) -> LoRA verdicts 4/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 vs scSemi-5 coverage_dm (shared-draw means; LoRA-better draws/n; verdict): ImMicro 0.966 vs 0.284 (5/5, lora); Sepsis 0.834 vs 0.158 (5/5, lora); Imperial 0.863 vs 0.152 (5/5, lora); Giroux 0.974 vs 0.238 (5/5, lora); Ji 0.908 vs 0.150 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 vs scSemi-5 precision_dm (shared-draw means; LoRA-better draws/n; verdict): ImMicro 0.975 vs 0.829 (5/5, lora); Sepsis 0.914 vs 0.504 (5/5, lora); Imperial 0.881 vs 0.429 (5/5, lora); Giroux 0.995 vs 0.426 (5/5, lora); Ji 0.974 vs 0.564 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 vs zero-shot + calibration coverage (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.792 vs 0.535 (5/5, lora); Sepsis 0.694 vs 0.428 (5/5, lora); Imperial 0.737 vs 0.634 (5/5, lora); Giroux 0.961 vs 0.944 (5/5, lora); Ji 0.707 vs 0.114 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json (arms lora5, zs_cal)"
+    },
+    {
+     "value": "LoRA-5 vs zero-shot + calibration precision (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.952 vs 0.904 (5/5, lora); Sepsis 0.906 vs 0.899 (3/5, split); Imperial 0.853 vs 0.845 (3/5, split); Giroux 1.000 vs 0.996 (4/5, lora); Ji 0.978 vs 0.782 (5/5, lora) -> LoRA verdicts 3/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json (arms lora5, zs_cal)"
+    },
+    {
+     "value": "LoRA-5 vs zero-shot + calibration comp_l1 (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.176 vs 0.203 (5/5, lora); Sepsis 0.466 vs 0.446 (2/5, split); Imperial 0.503 vs 0.506 (2/5, split); Giroux 0.256 vs 0.288 (2/5, split); Ji 0.513 vs 0.514 (3/5, split) -> LoRA verdicts 1/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json (arms lora5, zs_cal)"
+    },
+    {
+     "value": "LoRA-5 vs zero-shot + calibration coverage_dm (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.966 vs 0.780 (5/5, lora); Sepsis 0.834 vs 0.658 (5/5, lora); Imperial 0.863 vs 0.681 (5/5, lora); Giroux 0.974 vs 0.937 (5/5, lora); Ji 0.908 vs 0.357 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json (arms lora5, zs_cal)"
+    },
+    {
+     "value": "LoRA-5 vs zero-shot + calibration precision_dm (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.975 vs 0.940 (5/5, lora); Sepsis 0.914 vs 0.909 (3/5, split); Imperial 0.881 vs 0.868 (3/5, split); Giroux 0.995 vs 0.989 (5/5, lora); Ji 0.974 vs 0.658 (5/5, lora) -> LoRA verdicts 3/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json (arms lora5, zs_cal)"
+    },
+    {
+     "value": "LoRA-5 vs zero-shot (real bulk) coverage (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.792 vs 0.190 (5/5, lora); Sepsis 0.694 vs 0.076 (5/5, lora); Imperial 0.737 vs 0.114 (5/5, lora); Giroux 0.961 vs 0.472 (5/5, lora); Ji 0.707 vs 0.066 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json (arms lora5, zs_raw)"
+    },
+    {
+     "value": "LoRA-5 vs zero-shot (real bulk) precision (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.952 vs 0.677 (5/5, lora); Sepsis 0.906 vs 0.625 (5/5, lora); Imperial 0.853 vs 0.500 (5/5, lora); Giroux 1.000 vs 0.980 (5/5, lora); Ji 0.978 vs 0.799 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json (arms lora5, zs_raw)"
+    },
+    {
+     "value": "LoRA-5 vs zero-shot (real bulk) comp_l1 (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.176 vs 0.445 (5/5, lora); Sepsis 0.466 vs 0.510 (5/5, lora); Imperial 0.503 vs 0.806 (5/5, lora); Giroux 0.256 vs 0.351 (5/5, lora); Ji 0.513 vs 0.721 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json (arms lora5, zs_raw)"
+    },
+    {
+     "value": "LoRA-5 vs zero-shot (real bulk) coverage_dm (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.966 vs 0.213 (5/5, lora); Sepsis 0.834 vs 0.073 (5/5, lora); Imperial 0.863 vs 0.151 (5/5, lora); Giroux 0.974 vs 0.549 (5/5, lora); Ji 0.908 vs 0.199 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json (arms lora5, zs_raw)"
+    },
+    {
+     "value": "LoRA-5 vs zero-shot (real bulk) precision_dm (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.975 vs 0.671 (5/5, lora); Sepsis 0.914 vs 0.595 (5/5, lora); Imperial 0.881 vs 0.561 (5/5, lora); Giroux 0.995 vs 0.996 (2/5, split); Ji 0.974 vs 0.480 (5/5, lora) -> LoRA verdicts 4/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json (arms lora5, zs_raw)"
+    },
+    {
+     "value": "coverage cohort means over all draws: LoRA-5 ImMicro 0.792, Sepsis 0.694, Imperial 0.737, Giroux 0.961, Ji 0.707; scSemi-5 ImMicro 0.036, Sepsis 0.080, Imperial 0.059, Giroux 0.607, Ji 0.145; zero-shot + calibration ImMicro 0.535, Sepsis 0.428, Imperial 0.634, Giroux 0.944, Ji 0.114; zero-shot ImMicro 0.190, Sepsis 0.076, Imperial 0.114, Giroux 0.472, Ji 0.066",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 minus zero-shot + calibration composition L1, per-donor Wilcoxon (draw-averaged): ImMicro -0.027, n=107, p=2.2e-10; Sepsis +0.018, n=82, p=0.79; Imperial +0.016, n=57, p=0.38; Giroux -0.065, n=8, p=0.38; Ji -0.012, n=20, p=0.7 -> gain in 1/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/per_donor.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/folds.csv"
+    },
+    {
+     "value": "LoRA-5 minus zero-shot (real bulk) composition L1, per-donor Wilcoxon (draw-averaged): ImMicro -0.270, n=107, p=2.2e-18; Sepsis -0.044, n=82, p=0.15; Imperial -0.348, n=57, p=1.6e-08; Giroux -0.107, n=8, p=0.039; Ji -0.232, n=20, p=0.017 -> gain in 4/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/per_donor.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/folds.csv"
+    },
+    {
+     "value": "scSemiProfiler draws used / LoRA draws: ImMicro 5/5, Sepsis 5/5, Imperial 5/5, Giroux 5/5, Ji 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec09_scsemi_status.csv"
+    },
+    {
+     "value": "training pairs per draw: ImMicro 5, Sepsis 5, Imperial 12–15, Giroux 12–14, Ji 7–9; test pairs: ImMicro 102, Sepsis 77, Imperial 142–145, Giroux 10–12, Ji 24–26",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/fewshot_n5/DRAWS.json (n_train_rows, n_test_rows)"
+    },
+    {
+     "value": "LoRA r = 16; 3000 fixed steps; base runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt; sampling: test donors only, 1,500 cells each, seed 20260927, DDIM 50, EMA, Bernoulli read-out",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fewshot_n5/draw0/lora/RUN.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/README.md"
+    },
+    {
+     "value": "P/C definition: precision/coverage/density (PCA-50 + k = 10 balls fitted on the scored donors' observed R1 cells); PCA components in every summary.json = 50",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py"
+    }
+   ]
+  },
+  {
+   "title": "5 donors: LoRA vs scSemiProfiler — disease signal",
+   "layout": "figure_keywords",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_fewpair_disease.png"
+   ],
+   "keywords": [
+    "LoRA-5 > scSemi-5: DEG 2/4, logFC r 2/4",
+    "Spearman or limma: broadcast ahead 3/4",
+    "Split-half ceiling 0.96–0.99: not limiting"
+   ],
+   "footnote": "Same draws and verdict rule as the '5 donors: LoRA vs scSemiProfiler — cells' slide; DEG tie = half the draws equal or mean gap < 1 gene. Rank and threshold-free checks (scores_contrast/, tools/contrast_extra.py): Spearman r of the same logFC vectors; split-half ceiling = observed cells of each scored sample split in two halves (5 seeds), r of half-A vs half-B logFC, Spearman-Brown corrected to full data (noise-free ceiling); limma-voom top-50 = edgeR TMM + voom + limma eBayes on the same donor x type pseudobulks, BH FDR < 0.05, top 50 by |logFC|; grey tick = chance overlap (hypergeometric mean) of that arm's lists. Repeated samples of one patient (Imperial, Giroux, Ji) enter both tests as separate samples, as in the scorer. Sepsis: Spearman LoRA-5 0.22 / scSemi-5 0.16 / broadcast 0.33, limma top-50 LoRA-5 16.2 / scSemi-5 11.4 / broadcast 35.4 (chance 2.2), ceiling 0.99; Imperial: Spearman LoRA-5 0.55 / scSemi-5 0.37 / broadcast 0.36, limma top-50 LoRA-5 102.0 / scSemi-5 35.2 / broadcast 59.6 (chance 3.1), ceiling 0.97; Giroux: Spearman LoRA-5 0.19 / scSemi-5 0.27 / broadcast 0.38, limma top-50 LoRA-5 0.8 / scSemi-5 1.6 / broadcast 14.8 (chance 0.5), ceiling 0.97; Ji: Spearman LoRA-5 0.29 / scSemi-5 0.09 / broadcast 0.12, limma top-50 LoRA-5 3.0 / scSemi-5 0.6 / broadcast 6.2 (chance 1.4), ceiling 0.96. Earlier slide lines: logFC r: LoRA-5 > calibrated zero-shot 4/4; Giroux: broadcast r beats all arms. logFC r = mean over T/B/Mono/NK of case-vs-control log2FC r (generated vs observed); top-50 DEG = Welch+BH overlap summed over 5 types (max 250; Giroux 1–63, Ji 75–250 per draw). Giroux test = 2 vs 2 subjects per draw. LoRA-5-better draws (verdict): vs scSemi-5 logFC r Sepsis split 3/5, Imperial lora 5/5, Giroux scSemi-5 0/5, Ji lora 5/5; DEG Sepsis lora 5/5, Imperial lora 5/5, Giroux tie 1/5, Ji tie 1/5. Vs zero-shot + calibration: logFC r Sepsis lora 4/5, Imperial lora 5/5, Giroux lora 4/5, Ji lora 5/5; DEG Sepsis lora 4/5, Imperial lora 5/5, Giroux tie 1/5, Ji tie 1/5. Vs zero-shot (real bulk): logFC r Sepsis lora 5/5, Imperial lora 5/5, Giroux split 3/5, Ji lora 5/5; DEG Sepsis lora 4/5, Imperial lora 5/5, Giroux tie 1/5, Ji tie 1/5. Broadcast = the input real bulk's own logFC. Giroux: moderate vs mild subjects are 4F/0M vs 0F/5M (scored; all paired subjects 4F/1M vs 0F/5M; sex from bulk chrY expression = sc = GEO), so its disease metrics (logFC r, partial r, top-50 DEG, broadcast) exclude 196 sex-linked genes (43 chrY non-PAR + 153 X-inactivation escape / variable-escape genes of Tukiainen et al. 2017; PAR genes kept), 65 of them scoring genes; same labels and cells as before (scores_nosex/giroux2022/). Scores: scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/.",
+   "footnote_short": "Giroux: sex-linked genes excluded (severity confounded with sex: 4F/0M vs 0F/5M). Top-50 DEG over 5 types.",
+   "numbers": [
+    {
+     "value": "Giroux sex by contrast arm (subjects, F/M): scored moderate 4F/0M vs mild 0F/5M; all paired 4F/1M vs 0F/5M",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/features.npz (sex_bulk_expr = sex_sc_expr = sex_geo); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/folds.csv"
+    },
+    {
+     "value": "Giroux sex-linked genes excluded from the disease metrics: 196 listed (43 chrY non-PAR + 153 X escape), 65 of 5563 scoring genes",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/sex_linked_genes_exclude.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/BUILD.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json (gene_exclusion)"
+    },
+    {
+     "value": "Top-50 DEG LoRA-5 vs scSemi-5 (shared-draw means; LoRA-better / tied draws; verdict): Sepsis 16.4 vs 5.2 (5/5, 0 tied, lora); Imperial 113.6 vs 46.8 (5/5, 0 tied, lora); Giroux 0.2 vs 0.0 (1/5, 4 tied, tie); Ji 0.2 vs 0.0 (1/5, 4 tied, tie)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/summary.json and contrast.csv (Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/)"
+    },
+    {
+     "value": "Top-50 DEG LoRA-5 vs zero-shot + calibration (shared-draw means; LoRA-better / tied draws; verdict): Sepsis 16.4 vs 9.4 (4/5, 0 tied, lora); Imperial 113.6 vs 103.8 (5/5, 0 tied, lora); Giroux 0.2 vs 0.0 (1/5, 4 tied, tie); Ji 0.2 vs 0.0 (1/5, 4 tied, tie)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/summary.json and contrast.csv (Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/)"
+    },
+    {
+     "value": "Top-50 DEG LoRA-5 vs zero-shot (real bulk) (shared-draw means; LoRA-better / tied draws; verdict): Sepsis 16.4 vs 10.0 (4/5, 0 tied, lora); Imperial 113.6 vs 105.6 (5/5, 0 tied, lora); Giroux 0.2 vs 0.0 (1/5, 4 tied, tie); Ji 0.2 vs 0.0 (1/5, 4 tied, tie)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/summary.json and contrast.csv (Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/)"
+    },
+    {
+     "value": "logFC r LoRA-5 vs scSemi-5 (shared-draw means; LoRA-better draws; verdict): Sepsis 0.350 vs 0.402 (3/5, split); Imperial 0.749 vs 0.562 (5/5, lora); Giroux 0.297 vs 0.397 (0/5, other); Ji 0.333 vs 0.153 (5/5, lora)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/summary.json and contrast.csv (Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/)"
+    },
+    {
+     "value": "logFC r LoRA-5 vs zero-shot + calibration (shared-draw means; LoRA-better draws; verdict): Sepsis 0.350 vs 0.096 (4/5, lora); Imperial 0.749 vs 0.676 (5/5, lora); Giroux 0.297 vs 0.228 (4/5, lora); Ji 0.333 vs 0.140 (5/5, lora)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/summary.json and contrast.csv (Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/)"
+    },
+    {
+     "value": "logFC r LoRA-5 vs zero-shot (real bulk) (shared-draw means; LoRA-better draws; verdict): Sepsis 0.350 vs -0.024 (5/5, lora); Imperial 0.749 vs 0.638 (5/5, lora); Giroux 0.297 vs 0.255 (3/5, split); Ji 0.333 vs 0.087 (5/5, lora)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/summary.json and contrast.csv (Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/)"
+    },
+    {
+     "value": "Sepsis broadcast logFC r 0.320 vs best arm 0.402; broadcast DEG 20.0 vs best arm 16.4 (means over all draws; arms: zero-shot, zero-shot + calibration, scSemi-5, LoRA-5)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fewshot_n5/draw<j>{,_scsemi5}/summary.json"
+    },
+    {
+     "value": "Imperial broadcast logFC r 0.656 vs best arm 0.749; broadcast DEG 74.8 vs best arm 113.6 (means over all draws; arms: zero-shot, zero-shot + calibration, scSemi-5, LoRA-5)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/fewshot_n5/draw<j>{,_scsemi5}/summary.json"
+    },
+    {
+     "value": "Giroux broadcast logFC r 0.492 vs best arm 0.397; broadcast DEG 0.0 vs best arm 0.2 (means over all draws; arms: zero-shot, zero-shot + calibration, scSemi-5, LoRA-5)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/fewshot_n5/draw<j>{,_scsemi5}/summary.json"
+    },
+    {
+     "value": "Ji broadcast logFC r 0.234 vs best arm 0.333; broadcast DEG 1.0 vs best arm 0.2 (means over all draws; arms: zero-shot, zero-shot + calibration, scSemi-5, LoRA-5)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/fewshot_n5/draw<j>{,_scsemi5}/summary.json"
+    },
+    {
+     "value": "DEG maximum per draw: Sepsis 250, Imperial 250, Giroux 1–63, Ji 75–250",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json (deg_top50_max; Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex)"
+    },
+    {
+     "value": "Giroux test subjects per draw: 2 vs 2 (moderate vs mild); test pairs 10–12",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fewshot_n5/DRAWS.json (train_donors); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/folds.csv (group)"
+    }
+   ]
+  },
+  {
+   "title": "5-fold CV: train on the other 4 folds",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_fivefold.png"
+   ],
+   "keywords": [
+    "LoRA tops coverage 5/5, logFC r 3/4",
+    "Ji whole blood: LoRA 0.86, others 0.06–0.17",
+    "Broadcast ahead: Sepsis, Giroux"
+   ],
+   "footnote": "Donor-level 5-fold CV; each pair scored once, by the fold model that never trained on its donor (one pooled call per cohort). LoRA r=16 on the real bulk of the other 4 folds' training donors, early stop on inner-val donors. Zero-shot = base model without fine-tuning, fed the test pair's real bulk as measured; zero-shot + calibration = the same model fed gene-wise calibrated bulk (alpha fitted on the fold's training donors); sc-only fine-tune (+ calibration) = full fine-tune on training donors' sc pseudobulk, fed calibrated bulk. scSemiProfiler, 5-fold CV = scSemiProfiler with every training donor of the fold (inner-val included) as representatives, scored for the same pairs and reference cells (ImMicro, Sepsis, Giroux, Ji). Base f01 6k·1x·E16. LoRA best of 5 arms: coverage 5/5, logFC r 3/4, top-50 DEG 4/4. Broadcast = raw real bulk. Sepsis DEG from pooled_deg. Giroux: moderate vs mild subjects are 4F/0M vs 0F/5M (scored; all paired subjects 4F/1M vs 0F/5M; sex from bulk chrY expression = sc = GEO), so its disease metrics (logFC r, partial r, top-50 DEG, broadcast) exclude 196 sex-linked genes (43 chrY non-PAR + 153 X-inactivation escape / variable-escape genes of Tukiainen et al. 2017; PAR genes kept), 65 of them scoring genes; same labels and cells as before (scores_nosex/giroux2022/). Scores: scores/<cohort>/pooled/summary.json.",
+   "footnote_short": "Donor-level 5-fold CV. Giroux: sex-linked genes excluded (severity confounded with sex: 4F/0M vs 0F/5M).",
+   "numbers": [
+    {
+     "value": "LoRA best of 5 arms: coverage 5/5, logFC r 3/4, top-50 DEG 4/4",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/pooled/summary.json (Sepsis DEG: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled_deg/summary.json; Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json)"
+    },
+    {
+     "value": "Ji coverage: zero-shot 0.055, zero-shot + calibration 0.106, sc-only (+ calibration) 0.113, LoRA 0.857",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled/summary.json"
+    },
+    {
+     "value": "Giroux logFC r: broadcast 0.575 vs LoRA 0.461; DEG broadcast 5 vs LoRA 5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json"
+    },
+    {
+     "value": "LoRA logFC r vs broadcast: Sepsis 0.527 vs 0.316, Imperial 0.819 vs 0.661, Giroux 0.461 vs 0.575, Ji 0.479 vs 0.240",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/pooled/summary.json (Sepsis DEG: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled_deg/summary.json; Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json)"
+    },
+    {
+     "value": "coverage LoRA / zero-shot + calibration / zero-shot / sc-only (+ calibration): ImMicro 0.784 / 0.527 / 0.192 / 0.623, Sepsis 0.829 / 0.431 / 0.067 / 0.726, Imperial 0.850 / 0.639 / 0.112 / 0.555, Giroux 0.928 / 0.906 / 0.281 / 0.908, Ji 0.857 / 0.106 / 0.055 / 0.113",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/pooled/summary.json (Sepsis DEG: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled_deg/summary.json; Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json)"
+    },
+    {
+     "value": "logFC r LoRA / zero-shot + calibration / zero-shot / sc-only (+ calibration): Sepsis 0.527 / 0.123 / -0.012 / 0.296, Imperial 0.819 / 0.679 / 0.644 / 0.808, Giroux 0.461 / 0.269 / 0.334 / 0.344, Ji 0.479 / 0.142 / 0.084 / 0.245",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/pooled/summary.json (Sepsis DEG: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled_deg/summary.json; Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json)"
+    },
+    {
+     "value": "top-50 DEG LoRA / zero-shot + calibration / zero-shot / sc-only (+ calibration): Sepsis 23 / 11 / 9 / 15, Imperial 143 / 111 / 106 / 129, Giroux 5 / 0 / 1 / 0, Ji 15 / 0 / 0 / 0",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/pooled/summary.json (Sepsis DEG: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled_deg/summary.json; Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json)"
+    },
+    {
+     "value": "scSemiProfiler, 5-fold CV: coverage / logFC r / top-50 DEG (n/a = no contrast or rescore pending): ImMicro 0.038 / n/a / n/a, Sepsis 0.096 / 0.435 / 6, Giroux 0.354 / 0.537 / 0, Ji 0.167 / 0.273 / 0",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/scsemi_cv_20261002/pooled/summary.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_cv_20261002/pooled/summary.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/scsemi_cv_20261002/pooled/summary.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/scsemi_cv_20261002/pooled/summary.json"
+    },
+    {
+     "value": "Pooled n (pairs / donors): ImMicro 107/107, Sepsis 82/82, Imperial 157/57, Giroux 24/9, Ji 33/20",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/pooled/summary.json (n_donors); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/fewshot_n5/DRAWS.json"
+    },
+    {
+     "value": "early stopping: About 10 % of each fold's training donors are inner-validation, used only for early stopping",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/README.md"
+    }
+   ]
+  }
+ ],
+ "scripts": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/sec09_paired_validation.py"
+ ],
+ "generated_from": "tools/sec09_paired_validation.py (rerun to refresh; do not edit by hand)",
+ "scsemi_draws_used": "25/25"
+}

	@@ -0,0 +1,53 @@

+{
+ "section": "S-deconvolution",
+ "scripts": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/secS_deconvolution.py"
+ ],
+ "generated_from": "tools/secS_deconvolution.py (rerun to refresh; do not edit by hand)",
+ "slides": [
+  {
+   "title": "Deconvolution with the same pairs: composition",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/secS_deconv_composition.png"
+   ],
+   "keywords": [
+    "PBISC closer than BayesPrism in 22/25 draws, than CIBERSORTx in 24/25",
+    "Deconvolution misreads real bulk",
+    "5-fold: PBISC lowest in 4 of 5 cohorts"
+   ],
+   "footnote_short": "Same donors, truth and scorer as PBISC. Reference = the paired donors' cells.",
+   "footnote": "Supplementary. Bulk deconvolution given the same paired donors as PBISC LoRA, on the paired benchmark's own splits, observed truth and scorer: 5-donor draws (reference = the draw's 5 training donors' observed cells, mixture = the test samples' real bulk) and 5-fold CV (reference = each fold's LoRA training + inner-validation pairs; pooled). BayesPrism: recommended gene set (protein-coding minus chrX/Y/M and ribosomal genes, 15-19k), reference states = gate | AIFI L2; its better theta (initial or final) in cell units is shown. CIBERSORTx: official Docker images (x86, run under qemu emulation on server_1), single-cell reference mode with S-mode batch correction (up to 400 reference cells per type), fractions in cell units (divided by each type's mean UMI per reference cell). CIBERSORTx HiRes gives per-sample cell-type expression for the genes it imputes per type (others are written as 1 and count as zero here); it imputed no gene of the four contrast types in 1 Ji ChILI and 2 Giroux draws, which therefore have no CIBERSORTx disease score. Composition L1 over the six-type gate, lower is better. 5-fold: PBISC has the lowest L1 except in Giroux (scSemiProfiler); scSemiProfiler bars appear as its 5-fold runs finish ('n/a' = still running). Pipeline check: on pseudobulk mixtures BayesPrism recovers the observed mRNA shares (e.g. T 0.39 vs 0.38), so the error comes from real bulk. Source: plans/bayesprism_paired_20261006/results/RESULTS_full.md, RESULTS_cibersortx.md.",
+   "numbers": [
+    {
+     "value": "ImMicro: 5 donors L1 PBISC 0.176 / BayesPrism 0.537 / CIBERSORTx 0.491; 5-fold PBISC 0.162 / BayesPrism 0.575 / CIBERSORTx 0.507 / scSemiProfiler 0.217; Sepsis: 5 donors L1 PBISC 0.466 / BayesPrism 0.446 / CIBERSORTx 0.582; 5-fold PBISC 0.362 / BayesPrism 0.475 / CIBERSORTx 0.607 / scSemiProfiler 0.502; Ji ChILI: 5 donors L1 PBISC 0.513 / BayesPrism 0.893 / CIBERSORTx 0.827; 5-fold PBISC 0.504 / BayesPrism 0.883 / CIBERSORTx 0.914 / scSemiProfiler 0.575; Imperial: 5 donors L1 PBISC 0.503 / BayesPrism 0.845 / CIBERSORTx 0.646; 5-fold PBISC 0.376 / BayesPrism 0.887 / CIBERSORTx 0.592 / scSemiProfiler running; Giroux: 5 donors L1 PBISC 0.256 / BayesPrism 1.455 / CIBERSORTx 0.669; 5-fold PBISC 0.258 / BayesPrism 0.878 / CIBERSORTx 0.591 / scSemiProfiler 0.243",
+     "source": "data/secS_deconvolution.csv"
+    }
+   ]
+  },
+  {
+   "title": "Deconvolution with the same pairs: disease signal",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/secS_deconv_disease.png"
+   ],
+   "keywords": [
+    "logFC r: PBISC ahead in 15/20 draws (BayesPrism), 17/17 (CIBERSORTx)",
+    "Beyond bulk: PBISC ahead in 18/20 and 17/17",
+    "Top-50 DEG mixed: PBISC ahead in 6/20 and 6/17"
+   ],
+   "footnote_short": "5-donor draws, mean over draws. Partial r = signal beyond the bulk broadcast.",
+   "footnote": "Supplementary. Case-vs-control per-cell-type logFC (mean CP10K; T, B, Monocyte, NK) from BayesPrism's posterior cell-type expression Z and CIBERSORTx HiRes, scored with the benchmark's own functions (the recomputed bulk broadcast equals the stored one in every split); partial r = the part beyond the bulk broadcast; top-50 DEG = Welch, summed over types (many ties at 0 in Ji and Giroux). 5-donor draws, mean over draws with a score. Giroux excludes sex-linked genes, as everywhere in the deck. CIBERSORTx: official Docker images (x86, run under qemu emulation on server_1), single-cell reference mode with S-mode batch correction (up to 400 reference cells per type), fractions in cell units (divided by each type's mean UMI per reference cell). CIBERSORTx HiRes gives per-sample cell-type expression for the genes it imputes per type (others are written as 1 and count as zero here); it imputed no gene of the four contrast types in 1 Ji ChILI and 2 Giroux draws, which therefore have no CIBERSORTx disease score. Source: plans/bayesprism_paired_20261006/results/RESULTS_full.md, RESULTS_cibersortx.md.",
+   "numbers": [
+    {
+     "value": "Sepsis: logFC r PBISC 0.350 / BayesPrism 0.241 / CIBERSORTx 0.069 / broadcast 0.320; partial r 0.305 / 0.095 / -0.010; DEG 16.4 / 27.0 / 25.4 / 20.0; Ji ChILI: logFC r PBISC 0.333 / BayesPrism 0.193 / CIBERSORTx 0.158 / broadcast 0.234; partial r 0.300 / 0.032 / 0.005; DEG 0.2 / 2.0 / 0.0 / 1.0; Imperial: logFC r PBISC 0.749 / BayesPrism 0.598 / CIBERSORTx 0.283 / broadcast 0.656; partial r 0.603 / 0.187 / 0.061; DEG 113.6 / 72.4 / 30.8 / 74.8; Giroux: logFC r PBISC 0.297 / BayesPrism 0.371 / CIBERSORTx 0.095 / broadcast 0.492; partial r 0.189 / 0.117 / 0.029; DEG 0.2 / 0.2 / 0.0 / 0.0",
+     "source": "data/secS_deconvolution.csv"
+    },
+    {
+     "value": "draws where PBISC LoRA-5 beats BayesPrism: logFC r 15/20, partial r 18/20, top-50 DEG 6 (BayesPrism ahead 8, ties 6); beats CIBERSORTx: logFC r 17/17, partial r 17/17, top-50 DEG 6 (CIBERSORTx ahead 4, ties 7)",
+     "source": "plans/bayesprism_paired_20261006/results/TABLE_fewshot_full.csv, TABLE_fewshot_cibersortx.csv"
+    }
+   ]
+  }
+ ]
+}